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1 #!/bin/bash
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2 input=$1
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3 output=$2
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4 outDir=$3
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5 mkdir $outDir
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6 EOL=$4
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7 mismatches=$5
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8 partial=$6
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9 name=$(basename "$7")
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10 ext="${name##*.}"
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11 name="${name%.*}"
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12 prefix=$name"_"
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13 dir="$(cd "$(dirname "$0")" && pwd)"
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14
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15 for ((i=8;i<=$#;i=i+2))
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16 do
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17 j=$((i+1))
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18 echo -e "${!i}\t${!j}" >> $outDir/barcodes.txt
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19 done
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20
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21 cd $outDir
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22 echo "$3"
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23 result=`$dir/sff2fastq $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial`
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24 echo "$result" | tail -n +2 | sed 's/\t/,/g' > output.txt
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25 echo "<html><head><title>$name demultiplex</title></head><body><table border='1'><thead><tr><th>ID</th><th>Count</th><th>FASTQ</th><th>FASTA</th></tr></thead><tbody>" >> $output
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26 ls
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27 while IFS=, read barcode count location
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28 do
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29 if [ "total" == "$barcode" ]
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30 then
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31 echo "<tr><td>$barcode</td><td>$count</td><td></td><td></td></tr>" >> $output
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32 break
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33 fi
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34 file=$name"_"$barcode
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35 cat $file.fastq | perl -e '$i=0;while(< >){if(/^\@/&&$i==0){s/^\@/\>/;print;}elsif($i==1){print;$i=-3}$i++;}' > $file.fasta
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36 cat $file.fastq
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37 echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td></tr>" >> $output
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38 done < output.txt
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39 echo "</tbody></body></html>" >> $output
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